Fàbregas boarded a plane to Barcelona at 7.30pm last night and, subject to a medical and confirmation of personal terms, will be unveiled formally by the reigning European champions at 1pm today.

It will bring to an end one of the longest-running transfer sagas in football, but also raise more questions over a youth policy at Arsenal that has always depended on keeping the club’s best players for the peak years of the careers.

Fabregas is expected to be followed out of Arsenalby Samir Nasri this week, with Manchester City ready to meet an asking price of £23 million.

Barcelona were last night claiming they will only have to pay €14.5 million up front for Fabregas, with a further €14.5 million to be paid in October. It is then understood that

€1 million will be released every year until the end of his contract in 2016. Providing Fabregas wins one Champions League and two La Liga titles over the next five years, Arsenal will receive a further €6 million. This takes the overall potential fee to €40 million (£35 million).

Arsenal had been hoping for a payment of £40 million but have ultimately decided that it is better not to keep an unhappy player.

The club are well aware that Fabregas, 24, might have attracted a fee closer to £50 million on the open market – there was also interest from Manchester City and Chelsea — but that he wanted to join only one club.

Arsenal issued a statement at half-time of last night’s Spanish Super Cup between Barcelona and Real Madrid to confirm that they had reached “agreement in principle” to sell Fabregas. Arsène Wenger stressed in the statement that he had wanted to keep Fabregas. His disappointment also appeared evident by his offering only a brief sentence of thanks to Fabregas.

“We have been clear that we didn’t want Cesc to leave and that remains the case,” said Wenger. “However, we understand Cesc’s desire to move to his hometown club and have now accepted an offer from Barcelona. We thank Cesc for his contribution at Arsenal and wish him future success.”

Arsenal added that the transfer was now subject to formal legal agreements and registration processes, together with Fabregas agreeing personal terms and passing a medical.

Fabregas has been so keen to join Barcelona that it is understood that he is even prepared to accept a pay-cut on his £120,000-a-week salary to help fund the deal. It is also believed that he will waive a four-year loyalty bonus, worth £4 million, from Arsenal.

The loss of Fabregas clearly represents a massive blow to Wenger, although that can be partially softened by the fact that Arsenal did pay just £700,000 in compensation to sign him from Barcelona as a 16 year-old.

Fabregas has since gained vast first-team experience at Arsenal, making 303 appearances and becoming both the club’s youngest first-team player and goalscorer. He was made captain in 2008.

Pep Guardiola, the Barcelona manager, last night acknowledged his development when he said: “Cesc is today a better player thanks to Arsène Wenger and Arsenal.”

Yet there was always the suspicion that he wanted to return to Barcelona and he first informed Wenger of his desire to leave in May 2010.

Barcelona have had four offers rejected over the past 16 months, but did also launch a relentless public pursuit of Fabregas that has done considerable damage to their relationship with Arsenal. Yet that pressure, combined with the brutal truth that Fabregas wants to leave, forced Arsenal’s hand. Fabregas leaves England having won only the 2005 FA Cup during his time at Arsenal.